Health authorities have told residents not to eat more than two small portions of fish a week.

"It's scaring us because we eat barramundi, all kinds of fish, shark, stingray, shells. This is the place where most people do their fishing," Mr Rory said.

The burning was exposed by Indigenous residents, who complained about it to the NT Mines Department in 2014.

The federal and territory governments ordered Glencore to draw up a new environmental impact statement (EIS) proving it can manage the storage of the reactive rock in order to be permitted to continue expanding.

But the new statement has not allayed the fears of many Indigenous residents that the environment will be protected.

"We always talk to the mine, and they say, 'this will be done, and we'll get that sorted out,' but the dump's still smoking. I don't think it will ever stop," Mr Rory said.

Plan to leave reactive waste on river bank forever

In its EIS, Glencore has not put forward a new method of controlling the burning.

Instead, it is arguing that the method it has been using — gradually smothering spontaneous combustions on the dump with clay, and packing the waste more tightly behind clean rock — is starting to work.

"From time to time our waste rock does have the potential to react quite quickly and, really, it's managed on a day-to-day basis," said Sam Strohmayr, general manager of the mine.

"The areas that we have addressed are under control, and we continue to finish off other areas."

The company is promising to catch more contaminated water seeping through the dump with drainage leading to plastic-lined dams.

The most contentious part of Glencore's EIS is that it wants to leave 500 million tonnes of waste on the bank of the McArthur River forever.

It has rejected putting the waste back into the mining pit as too expensive, saying it would make the project unviable.

"You can't do everything, so the outcome that we've identified is the best outcome," Mr Strohmayr said.

"There are environmental risks with any option that you take up and we've weighed the environmental risks with the whole project."

River would flow through waste lake

Another contentious part of the proposal is to put some of the most reactive waste rock and all of the tailings into the mine pit at the end of mining and then flood that pit with water, creating a lake.

The company would eventually allow the diverted McArthur River to flow through the lake.

Mr Strohmayr has acknowledged there are a number of uncertainties in the whole project plan, including how long the pit lake water would have to be treated, and how well the burning can be controlled.

"We plan to start to do rehabilitation early, so you have the opportunity to see how the assumptions that you've made and the modelling that you've done in the EIS is actually bearing out," he said.

Mr Strohmayr said the company's estimates that 30 more years of mining and processing would be able to pay for up to 1,000 years of rehabilitation are based on variables including "metal prices, which we don't have any control over".

'Considerable concern' for residents and scientists

The Environmental Defenders Office (EDO) green group feels the NT Government has allowed itself to be backed into a corner because if it refuses the expansion plan, the company could walk away now without rehabilitating the site.

The Government has admitted to the ABC that it has only required Glencore to lodge a rehabilitation security bond sufficient to pay for managing the waste rock outside the pit, not putting the waste back in.

The EDO has written a submission on the EIS on behalf of Indigenous residents around Borroloola, arguing that the mine should be closed before its environmental problems snowball.

If the expansion goes ahead the company should not leave the waste in a mountain on the river bank, or connect a pit lake to the McArthur River, principal lawyer David Morris said.

"Flooding the pit, then allowing the McArthur River to retrace its old path, is something that has been cause for considerable concern for both Borroloola people but also from water experts and other scientists that we've had review the EIS," he said.

The group sought advice from Dr Gavin Mudd, RMIT University associate professor of environmental engineering.

"If you look at leaving hundreds of millions of tonnes of reactive waste above ground, the question is not if it's going to leach, the question is how much," he said.

"The best way to manage that is to put it back in the pit below the groundwater table."